phc-ingestion 0.10.20__py3-none-any.whl → 0.11.1__py3-none-any.whl

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Files changed (6) hide show
  1. ingestion/caris/util/metadata.py +3 -3
  2. ingestion/foundation/util/ga4gh.py +3 -3
  3. ingestion/generic/utils.py +0 -1
  4. {phc_ingestion-0.10.20.dist-info → phc_ingestion-0.11.1.dist-info}/METADATA +1 -1
  5. {phc_ingestion-0.10.20.dist-info → phc_ingestion-0.11.1.dist-info}/RECORD +6 -6
  6. {phc_ingestion-0.10.20.dist-info → phc_ingestion-0.11.1.dist-info}/WHEEL +0 -0
ingestion/caris/util/metadata.py CHANGED
@@ -106,10 +106,10 @@ def extract_metadata(data, prefix, files, source_file_id, log: Logger) -> dict:
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  patient = data["patientInformation"]
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  metadata["bodySiteSystem"] = "http://lifeomic.com/fhir/sequence-body-site"
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  metadata["reportID"] = get_report_id(test_details)
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- metadata["mrn"] = patient["mrn"]
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- metadata["patientLastName"] = patient["lastName"]
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+ metadata["mrn"] = patient["mrn"].strip()
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+ metadata["patientLastName"] = patient["lastName"].strip()
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- metadata["patientDOB"] = patient["dob"]
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+ metadata["patientDOB"] = patient["dob"].strip()
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  # Get physician info - ordering name, NPI, and facility
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  metadata["medFacilName"] = get_med_facil_name(physician_details)
ingestion/foundation/util/ga4gh.py CHANGED
@@ -180,7 +180,7 @@ def get_test_yml(
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  # Hard-code genome reference for FMI
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  genome_reference = "GRCh37"
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- mrn = get_mrn(pmi)
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+ mrn = get_mrn(pmi).strip()
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  trf = get_trf(sample)
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@@ -220,8 +220,8 @@ def get_test_yml(
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  "reportDate": reportDate,
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  "reportID": trf,
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  "mrn": mrn,
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- "patientDOB": get_date(pmi.get("DOB")),
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- "patientLastName": pmi.get("LastName"),
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+ "patientDOB": get_date(pmi.get("DOB")).strip(),
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+ "patientLastName": pmi.get("LastName").strip(),
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  "medFacilName": med_facil_info[0],
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  "medFacilID": med_facil_info[1],
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  "orderingMDName": ordering_md_info[0],
ingestion/generic/utils.py CHANGED
@@ -44,7 +44,6 @@ def check_manifest(manifest_file_path: str, case_id, log: Logger):
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  Optional("plasmaTumorFraction"): str,
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  Optional("cellPurity"): float,
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  Optional("hrdStatus"): str,
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- Optional("specimenIds"): list[str],
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  }
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  )
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{phc_ingestion-0.10.20.dist-info → phc_ingestion-0.11.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phc-ingestion
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- Version: 0.10.20
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+ Version: 0.11.1
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  Summary: Functions for LifeOmic PHC genomic ingestions
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  License: MIT
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  Author-email: LifeOmic Development <development@lifeomic.com>
{phc_ingestion-0.10.20.dist-info → phc_ingestion-0.11.1.dist-info}/RECORD RENAMED
@@ -8,7 +8,7 @@ ingestion/caris/util/hla.py,sha256=X_t6ngBRvmdG3m4I2_KnPFeWn3BaH-3IWHtOvDbS32A,7
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  ingestion/caris/util/ihc.py,sha256=1XfFJjvQq9E45cdPX4EPrg2VkXABxbMJP_BOgzA8z7g,13091
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  ingestion/caris/util/interpretation.py,sha256=CghNurqeVA5VTBBorU8-ZTN-PVNPnR8wrmTwKCH3568,555
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  ingestion/caris/util/json.py,sha256=aifO1hnZwNSS-ZtY20otyGbfIoc23w9HMWJ5D56lhFo,5020
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- ingestion/caris/util/metadata.py,sha256=a6NToMtGtIRrlMd3CQwq4IRjGGmIiBA9JFwsATjNEoQ,10287
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+ ingestion/caris/util/metadata.py,sha256=OaEG50FrYqyj1n9u9F3Qt17SX2K0cmIIzI6d8Assj64,10311
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  ingestion/caris/util/specimen_details.py,sha256=wDTIelrGelAuSljmE6dAoJRjb9kwrlhmB2f1_vcCiUc,2963
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  ingestion/caris/util/structural.py,sha256=EUcMIea_WnafoVmFLIyEqlJ_HtYIj_g6qkekXa7QNQs,4628
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  ingestion/caris/util/tests.py,sha256=mcG3A8TW81_sn2Bfoa-Gd6Q1sR3_R4FX2BNskD4DkJk,372
@@ -20,12 +20,12 @@ ingestion/foundation/process.py,sha256=mzKVVefGZD1HkEi0Hbb9eD_flwGp1S6SZ7FNXZpWn
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  ingestion/foundation/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ingestion/foundation/util/cnv.py,sha256=eyTn1lqbo0tmEacnqWuGATt1h9lllTlVlboT8n5C6Ao,4283
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  ingestion/foundation/util/fnv.py,sha256=B8tOREYsR45aIGdSj8SPpe7f3L8FlGaIhLe0DSNqCnc,6006
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- ingestion/foundation/util/ga4gh.py,sha256=RqyKuntH5Y-dRpr188i2hR8yc1F_An_8Z9DlGsFa0Sw,11779
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+ ingestion/foundation/util/ga4gh.py,sha256=GVHjMQNd7RaRg9qX7fStBcW5toLjvJCuHvu6hqm4tAo,11803
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  ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
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  ingestion/foundation/util/vcf_etl.py,sha256=GXV5JXswwdyHEEdPsM3Qq8tDPFkvZajrZn5chWgF53k,2266
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  ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
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- ingestion/generic/utils.py,sha256=_v3dKqlZK0S99_thSMD4ojkuFbBRWadBcS-RF-lTdJk,2862
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+ ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
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  ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
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  ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
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  ingestion/nebula/manifest_assembler.py,sha256=kcRSy6pixHkuVEK9QSoM-i6ZdLWMSYXw39eKGHvam34,7995
@@ -60,6 +60,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
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  ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
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  ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
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  ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
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- phc_ingestion-0.10.20.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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- phc_ingestion-0.10.20.dist-info/METADATA,sha256=O4v14ntrknbOIU1iPTEoO8kQ8uXVNnNYotDo8YDkQis,678
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- phc_ingestion-0.10.20.dist-info/RECORD,,
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+ phc_ingestion-0.11.1.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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+ phc_ingestion-0.11.1.dist-info/METADATA,sha256=ucEZCziomM9ANPMV8jqSBT5Huigd0UownHOnSKWqKdc,677
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+ phc_ingestion-0.11.1.dist-info/RECORD,,